Results

Data associated with the results presented here can be found at: https://github.com/courtois-neuromod/anat-processing/releases.

Brain

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Load data and plot it

dataset.load()
fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')

Spinal cord

Spinal cord cross-sectional area

Download data

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Load data plot it

dataset.load()

fig_spine = Plot(dataset, plot_name = 'new-fig')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'WM')

Gray matter cross-sectional area

White matter qMRI